Hi I was wondering if it is possible to alter the fade out effect at all. Currently the page fades out to the loader image then the loader image fades away pretty quickly even before the new page fades in.

no no I am not saying that, I am saying that AWS was not working on your site.
Whatever be the problem you are saying that can be solve and as I believe in support thread some already answered for this problem.

It appears to be some conflict with rocket loader from cloudflare. I have created a ticket with them to try and fix the issue. With it disabled I am able to make the loader stay on the page without fading setting opacity to 1.